Contacts of the strand formed by residues 435 - 440 (chain B) in PDB entry 1KHU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TRP 435 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A VAL* 3.6 29.2 - - + -
276B TYR* 3.5 1.9 - - - -
277B TYR* 2.7 84.9 + + + +
279B LEU 2.8 23.6 + - - -
280B ASN* 5.6 0.2 - - - -
413B ARG* 3.7 29.8 - - + -
414B MET 3.3 12.6 - - - +
415B SER* 3.8 3.4 - - - +
416B PHE* 4.7 1.6 - - - -
429B VAL* 3.6 36.7 + - + -
430B THR* 4.1 3.3 - - + +
432B THR* 3.3 34.8 - - - +
434B CYS* 1.3 74.6 - - - +
436B ILE* 1.3 85.3 + - - +
437B GLU* 4.1 4.3 - - + -
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Residues in contact with ILE 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ILE* 3.9 20.4 - - + -
275B VAL 3.1 17.3 - - - +
276B TYR* 3.8 20.2 - - + +
277B TYR* 4.8 0.4 - - - -
296B VAL* 4.2 27.8 - - + -
309B PHE* 4.6 1.3 - - + -
334B VAL* 4.5 2.0 - - + -
336B LEU* 5.0 0.4 - - + -
412B ILE 4.0 0.2 - - - +
413B ARG* 3.3 3.6 - - - -
414B MET* 2.8 67.0 + - + +
416B PHE* 4.2 15.3 - - + -
435B TRP* 1.3 88.2 - - - +
437B GLU* 1.3 61.2 + - - +
438B ILE* 4.3 11.2 - - + -
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Residues in contact with GLU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A SER* 3.3 35.5 + - - -
317A VAL* 5.5 0.5 - - - +
273B SER 3.9 0.3 - - - +
274B ILE* 3.3 5.2 - - - +
275B VAL* 3.0 34.6 + - + +
277B TYR* 3.6 22.7 + - + -
411B THR* 3.9 13.6 + - - -
412B ILE 3.4 4.3 - - - +
413B ARG* 3.1 36.2 + - + +
435B TRP* 4.1 11.5 - - + -
436B ILE* 1.3 75.4 - - - +
438B ILE* 1.3 65.2 - - - +
439B HIS* 3.8 18.1 + - + +
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Residues in contact with ILE 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B TRP* 5.3 1.8 - - + -
272B CYS* 4.2 17.9 - - + -
273B SER 3.6 3.4 - - - +
274B ILE* 4.1 26.5 - - + -
336B LEU* 3.7 24.7 - - + -
382B ILE* 5.0 4.3 - - + -
410B CYS 3.8 0.3 - - - +
411B THR* 3.0 7.4 - - - -
412B ILE* 2.6 55.7 + - + +
414B MET* 3.7 28.3 - - + -
436B ILE* 4.3 9.4 - - + -
437B GLU* 1.3 76.9 - - - +
439B HIS* 1.3 63.9 + - - +
440B LEU* 4.0 15.3 - - + +
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Residues in contact with HIS 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A LEU* 2.9 37.0 + - + -
314A LEU* 4.8 0.8 - - - -
315A SER* 3.0 23.4 + - - -
272B CYS* 3.2 3.9 - - - -
273B SER* 2.9 39.1 + - - +
275B VAL* 6.1 4.1 - - + +
410B CYS 3.7 2.2 - - - -
411B THR* 3.1 26.3 - - + +
437B GLU* 3.8 17.4 + - + +
438B ILE* 1.3 74.0 - - - +
440B LEU* 1.3 60.2 + - - +
441B HIS* 3.1 19.5 - - + -
444B LEU* 3.9 21.5 - - + -
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Residues in contact with LEU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B TRP* 3.7 37.9 - - + +
272B CYS* 4.1 5.4 - - + -
338B TYR* 6.0 0.7 - - + -
343B VAL* 4.2 12.6 - - + -
383B PHE* 4.7 15.7 - - + -
410B CYS* 2.9 28.8 + - - +
412B ILE* 3.8 26.5 - - + -
438B ILE* 4.0 16.8 - - + +
439B HIS* 1.3 69.2 - - - +
441B HIS* 1.3 66.0 + - - +
442B GLY 3.4 0.7 - - - -
443B PRO* 3.3 24.7 - - + +
444B LEU* 3.2 24.3 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il